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Urbanization-induced soil degradation poses a significant threat to the structural resilience and functional capacity of croplands, with profound implications for sustainable agriculture and ecosystem stability. Despite increasing concern, there remains a critical gap in comprehensive, quantitative assessments of how urbanization affects key indicators of soil degradation. This study investigates the influence of urbanization on soil structural integrity, health, and degradation level in corn-cultivated agroecosystems by comparing urban and non-urban farms across four soil types. We developed a comprehensive soil degradation index (CSDI) using total dataset (CSDI-TDS) and a minimum dataset (CSDI-MDS) approaches to evaluate physical and chemical soil degradation indicators. Urban soils exhibited significantly higher soil erodibility (18–25% increase in the K-factor) and heavy metal accumulation (12–102% increase) compared to non-urban counterparts, signaling compromised soil structure and resilience. The average CSDI-TDS and CSDI-MDS scores were elevated by 14–21% and 16–22%, respectively, in urban soils, indicating a marked intensification of degradation linked to urban dynamics. Variables such as modified clay ratio (MCR), soil stability index (SSI), soil organic carbon (SOC), and sodium adsorption ratio (SAR) were identified as primary indexes differentiating soil structural vulnerability in urban and non-urban settings. Corn productivity accounts for a relatively weak 22–25% of the variance in both the CSDI-MDS and CSDI-TDS, indicating a limited influence of CSDIs on crop performance. These findings highlight the utility of the CSDI, especially the CSDI-MDS, as a sensitive and responsive framework for assessing the impacts of urbanization on soil structural health and agroecosystem sustainability. This work contributes to the growing body of research aimed at reinforcing soil biophysical and chemical resilience under the dual pressures of land-use change and climate variability.